NEWS

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graphite 1.49.1

• Updated all pathway data.

graphite 1.47.1

• Removed Clipper support.
• Updated all pathway data.

graphite 1.45.1

• Updated all pathway data.

graphite 1.43.2

• Updated all pathway data.

graphite 1.41.2

• Updated all pathway data.

graphite 1.39.3

• Updated all pathway data.

graphite 1.37.1

• Removed Biocarta and NCI pathways.
• Added WikiPathways pathways.
• Updated all pathway data.

graphite 1.35.2

• Updated all pathway data.

graphite 1.33.1

• Updated all pathway data.

graphite 1.31.1

• Updated all pathway data.
• Removed HumanCyc pathways (database now requires subscription).

graphite 1.29.3

• Updated all pathway data.

graphite 1.27.6

• Updated all pathway data.
• Added PathBank database.

graphite 1.27.2

• Vignette describing mixed analysis with genes and metabolites.

graphite 1.25.9

• Updated all pathway data.

graphite 1.25.7

• cytoscapePlot returns an handle to the exported graph.

graphite 1.25.6

• Parallel versions of clipper and topologyGSA methods.

graphite 1.25.3

• Faster conversion of identifiers.

graphite 1.25.2

• Documentation fixes.
• Removed deprecated objects biocarta, humancyc, kegg, nci, panther, reactome.

graphite 1.25.1

• Export the pathwayURL function.

graphite 1.23.7

• Provide the URL of each pathway in its original database.
• New vignette describing pathway analysis of metabolic activities.

graphite 1.23.6

• Removed DEGraph support.

graphite 1.23.5

• runClipper gains an option to set the seed for random number generation.

graphite 1.23.3

• Metabolites in pathways.
• Multiple views of each pathway: proteins only, metabolites only or both.
• New databases: SMPDB and PharmGKB.
• Removed support for RCytoscape (by default, use RCy3).
• Conversion of metabolite identifiers.
• Faster conversion of idenfiers on multicore systems.

graphite 1.21.1

• Updated all pathway data.

graphite 1.19.3

• Updated all pathway data.

graphite 1.17.6

• Added celegans pathways from KEGG.

graphite 1.17.5

• Updated all pathway data.

graphite 1.17.4

• Cytoscape 3 support.

graphite 1.17.3

• Added the buildPathway function.

graphite 1.15.3

• Updated all pathway data.
• More descriptive edge types.
• Use the package "rappdirs" to select a directory for cached files.
• Updated all pathway data.
• More descriptive edge types.
• Use the package "rappdirs" to select a directory for cached files.

graphite 1.13.2

• Pathways for multiple species: see pathwayDatabases() output.
• Native pathway IDs.
• Removed SPIKE database.
• Deprecated objects: biocarta, humancyc, kegg, nci, panther, reactome.
• Deprecated functions: runClipperMulti, runDEGraphMulti, runTopologyGSAMulti.

graphite 1.11.4

• Updated Biocarta, KEGG, NCI, HumanCyc, Panther and Reactome data.

graphite 1.9.4

• Updated Biocarta, KEGG, NCI and Reactome data.
• New databases: HumanCyc and Panther.